Greetings! My partners and I got this homework. We're not specialized in bioinformatics or anything (pretty amateurs). And we're struggling with some tools. If there is a good soul who would help us my faith in humanity will be.. wait, I never loose faith in humanity, but we would be very thankful.

Our homework consist on the next..

Our data is paired end reads from mother, father and daughter (R1 and R2 of each), by mapping the 3 sets, compare to a proper reference genome and with the right strategies find sites with strong evidence of polymorphism.
Utilize VCF for analyzing SNPs, indel, MNP, complex (multiple internal alternative alleles), and the number of the 5 genes with the most polymorphic sites. Including results only when probabilities of a false positive are 1 on 10000 of the Qual column on VCF

The first steps involve data preparation for the downstream analysis. Each is described in the tutorial steps.

This set of learning tutorials might help as they cover the same steps in different analysis plus the overview can provide context for how to use the results (through the linked publications, technology summaries, etc): https://github.com/nekrut/galaxy/wiki

Also know that many tools are wrapped 3rd party applications. Reviewing the manual for these will almost certain help with the "why use them" questions.

If any steps remain unclear after reviewing the above, please let us know which and we can try to help more.